2-way adonis (PERMANOVA) incl interaction - how to test for main effects?

On 16/10/18 11:23, Torsten Hauffe wrote:

  "adonis2(speciesdataset~A*B, by="margin") but then only the effect of

the

interaction is tested."

This is not entirely correct.
adonis2(speciesdataset~A:B, by="margin") would test the interaction

alone.

~A*B unfolds to ~A+B+A:B

Well, it was correct: the only **marginal** effect in ~A+B+A:B is A:B (A
and B are not marginal), and by = "margin" will only analyse marginal
effects.

Cheers, Jari Oksanen

On Tue, 16 Oct 2018 at 11:51, Ellen Pape <ellen.pape at gmail.com> wrote:

Hi all,

I don't know whether this is the correct mailing group to address this
question:

I would like to perform a 2-way permanova analysis in R (using adonis in
vegan). By default you are performing sequential tests (by="terms"), so
when you have 2 or more factors, the order of these factors matter.
However, since I wanted to circumvent this, I chose for the option
by="margin" (adonis2(speciesdataset~A*B, by="margin")) but then only the
effect of the interaction is tested. On the "help page" of anova. cca it
says: "if you select by="margin" -> the current function only evaluates
marginal terms. It will, for instance, ignore main effects that are
included in interaction terms."


My question now is: can I somehow get the main effects tested anyhow,

when

the interaction term is not significant?

Thanks,
Ellen

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